SurfLayers

Overview

This is a program to compute intermediate surfaces between two boundary surfaces

SurfLayers computes new surfaces for a given number of cortical divisions
at intermediate distances by simple computation of the fraction
between the inner and outer-most surfaces (aka "equi-distant").
A single dividing surface would be halfway between the two surfaces.

Options

-spec SPEC_DSET      :dataset that is the SUMA specification file
                      describing input surfaces

-outdir DIRNAME      :new directory for output (default: surflayers)

-states IN OUT       :typically smoothwm, pial states to describe inner
                      and outer surfaces (default: "smoothwm pial")

-hemi  HH            :choose hemisphere: "lh", "rh" or "lh rh" (for both)

-n_intermed_surfs N  :total number of intermediate surfaces to create

-surf_A      SB      :inner boundary surface by filename (e.g. smoothwm.gii)

-surf_B      SA      :outer boundary surface by filename (e.g. pial.gii)

-surf_intermed_pref SIP  :name for interpolated surfaces
                      (default: isurf)

-echo                :run script with 'set echo' (i.e., verbosely)

-no_clean            :do not remove temp files (probably just for testing)

Notes

Output includes a new directory containing:
+ isurf.lh.01...n.gii -  interpolated surfaces numbered 1 to n
+ other files too if -spec option was utilized
+ a run*tcsh script to view the output directly

See also the quickspecSL program for creating a *.spec file.

For more information or questions, please contact:
  Salvatore (Sam) Torrisi (salvatore.torrisi@ucsf.edu)
  Daniel Glen (glend@mail.nih.gov)

Examples

1)

SurfLayers                       \
    -spec std.60.myspec.lh.spec  \
    -states "white pial"         \
    -n_intermed_surfs 3

2)

SurfLayers                       \
    -surf_A lh.white.gii         \
    -surf_B lh.pial.gii          \
    -n_intermed_surfs 3